Blooms of cyanobacteria have negative effects on aquatic organisms and even on human health, since many species can synthesize dangerous toxins. Studies on cyanobacteria and their potential toxicity have been very scarce in Chile and have been limited to lakes of the central zone. Recently, North-Patagonian lakes, although characterized by their low nutrient concentration and low productivity, revealed also the presence of blooms of cyanobacteria, mainly constituted by Microcystis and Dolichospermum species (former Anabaena sp.). To identify potential toxicological risk associated to these blooms, six North Patagonian lakes (Lakes Caburgua, Villarrica, Calafquen, Panguipulli, Ranco, and Puyehue) were sampled during the summer period and screened for the presence of cyanobacteria and different toxins. Our results revealed for the first time the presence of microcystins in all studied lakes, whereas other toxins such as cylindrospermopsin, saxitoxin, and anatoxin were negative for all sites. By applying a genomic approach, Cylindrospermopsis raciborskii was found in one lake (Lake Ranco) constituting the first report of this cyanobacterium in a Chilean lake. This study highlights the effectiveness of molecular methods as a first approach to describe cyanobacteria and their potential cyanotoxins in Chilean North-Patagonian lakes.